cERMIT v1.2 – the Evidence Ranked Motif Identification Tool

cERMIT v1.2

:: DESCRIPTION

cERMIT is a computationally efficient motif discovery tool based on analyzing genome-wide quantitative regulatory evidence.

::DEVELOPER

Uwe Ohler’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

  cERMIT

:: MORE INFORMATION

Citation:

Genome Biol. 2010;11(2):R19. doi: 10.1186/gb-2010-11-2-r19. Epub 2010 Feb 15.
Evidence-ranked motif identification.
Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, Ohler U.

PhyloCon v3b – Phylogenetic Consensus for Regulatory Motif Identification

PhyloCon v3b

:: DESCRIPTION

PhyloCon (Phylogenetic Consensus) combines phylogenetic data with coregulated genes to identify regulatory motifs. PhyloCon is a motif discovery program. It is derived from a well established program “Consensus”, with comparative genomic features added.  PhyloCon assumes a “multiple gene, multiple species” model. It takes into account both conservation among orthologous genes and co-regulation of genes within a species. This algorithm first aligns conserved regions of orthologous sequences into multiple sequence alignments, or profiles, then compares profiles representing non-orthologous sequences. Motifs emerge as common regions in these profiles. The program will determine the width of the pattern being sought.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhyloCon

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Dec 12;19(18):2369-80.
Combining phylogenetic data with co-regulated genes to identify regulatory motifs.
Wang T, Stormo GD.

EM-NM – Network Motif Identification in Stochastic Networks

EM-NM

:: DESCRIPTION

EM-NM is intended to implement the methodology for network motif identification in stochastic networks.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 EM-NM

:: MORE INFORMATION

Citation

Rui Jiang, Zhidong Tu, Ting Chen, and Fengzhu Sun.
Network Motif Identification in Stochastic Networks
Proc. Natl. Acad. Sci. USA, Vol.103, No.25, 9404~9409, 2006.

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